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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ), 'gf_id' => 'ORTHO05D001059', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ), 'data_identifier' => 'ORTHO05D001059', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001059', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '505', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03140' => 'bna', 'A03p07270' => 'bna', 'A06p36660' => 'bna', 'A07p30090' => 'bna', 'A07p38930' => 'bna', 'A09p05950' => 'bna', 'Aa31LG11G13950' => 'aar', 'Aa31LG1G21010' => 'aar', 'Aa31LG4G3160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1618' => 'aag', 'Actinidia17596' => 'ach', 'Actinidia18495' => 'ach', 'Actinidia26037' => 'ach', 'Actinidia26260' => 'ach', 'Actinidia39091' => 'ach', 'Ah.08g216600' => 'amhyb', 'Ah.10g034020' => 'amhyb', 'Ah.10g038090' => 'amhyb', 'AL1G29900' => 'aly', 'AL2G32510' => 'aly', 'AL6G26490' => 'aly', 'AL6G38200' => 'aly', 'Aqoxy316s003' => 'aox', 'Aqoxy3G00513' => 'aox', 'Aqoxy5G02739' => 'aox', 'Aqoxy7G01113' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0WCZ1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MF5PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8AEQ4X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KK0LLK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8SLK4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M0GYTU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG2K2N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S41I71' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY7AXN' => 'arhy', 'AT1G72820' => 'ath', 'AT5G15640' => 'ath', 'AT5G26200' => 'ath', 'ATR0598G353' => 'atr', 'ATR0693G187' => 'atr', 'ATR0827G045' => 'atr', 'Atru.chr1.3877' => 'acertr', 'Atru.chr1.3897' => 'acertr', 'Atru.chr4.3120' => 'acertr', 'Atru.chr7.1875' => 'acertr', 'Atru.chr8.521' => 'acertr', 'AUR62001504' => 'cqu', 'AUR62002579' => 'cqu', 'AUR62009099' => 'cqu', 'AUR62009495' => 'cqu', 'AUR62009866' => 'cqu', 'AUR62020573' => 'cqu', 'AUR62023175' => 'cqu', 'AUR62030001' => 'cqu', 'BcaB01g05035' => 'bca', 'BcaB03g15017' => 'bca', 'BcaB03g15683' => 'bca', 'BcaB04g19745' => 'bca', 'BcaB05g24779' => 'bca', 'BcaC03g18440' => 'bca', 'BcaC04g23606' => 'bca', 'BcaC08g45695' => 'bca', 'BcaC08g46720' => 'bca', 'BcaNung02807' => 'bca', 'BcaNung03975' => 'bca', 'BcaNung06750' => 'bca', 'BcaNung06785' => 'bca', 'BolC2t06712H' => 'bol', 'BolC3t13341H' => 'bol', 'BolC6t38573H' => 'bol', 'BolC6t39748H' => 'bol', 'BolC7t44716H' => 'bol', 'BolC9t53576H' => 'bol', 'BraA02t05284Z' => 'bra', 'BraA03t10049Z' => 'bra', 'BraA06t26589Z' => 'bra', 'BraA07t30646Z' => 'bra', 'BraA07t31447Z' => 'bra', 'BraA09t36237Z' => 'bra', 'C02p07870' => 'bna', 'C03p08340' => 'bna', 'C06p34640' => 'bna', 'C06p47080' => 'bna', 'C07p41840' => 'bna', 'C09p06530' => 'bna', 'CAN.G208.86' => 'can', 'CAN.G497.85' => 'can', 'CAN.G627.4' => 'can', 'CAN.G862.22' => 'can', 'CANSAT25G1488' => 'cansat', 'CANSAT56G2564' => 'cansat', 'CANSAT64G0812' => 'cansat', 'CARHR065740' => 'chi', 'CARHR187170' => 'chi', 'CARHR197680' => 'chi', 'Carub.0002s1966' => 'cru', 'Carub.0006s1379' => 'cru', 'Carub.0006s2398' => 'cru', 'Ca_00936_v3' => 'car', 'Ca_05019_v3' => 'car', 'Ca_15842_v3' => 'car', 'Ca_22736_v3' => 'car', 'CBR_g34720' => 'cbr', 'CBR_g52044' => 'cbr', 'Cc03_g00360' => 'ccan', 'Cc04_g01500' => 'ccan', 'Cc07_g04410' => 'ccan', 'Cc07_g04420' => 'ccan', 'Cc08_g01400' => 'ccan', 'CDE04G1154' => 'cde', 'CDE05G0473' => 'cde', 'CDE05G1705' => 'cde', 'CDE05G3147' => 'cde', 'CDE06G0501' => 'cde', 'CDE11G1222' => 'cde', 'Cfa003548' => 'cfa', 'Cfa018003' => 'cfa', 'Ciclev10005618m.g' => 'ccl', 'Ciclev10006822m.g' => 'ccl', 'Ciclev10008781m.g' => 'ccl', 'Ciclev10012200m.g' => 'ccl', 'Ciclev10024543m.g' => 'ccl', 'Ciclev10025998m.g' => 'ccl', 'CiPaw.01G131600' => 'cil', 'CiPaw.01G131900' => 'cil', 'CiPaw.02G137300' => 'cil', 'CiPaw.03G084900' => 'cil', 'CiPaw.15G088700' => 'cil', 'ClCG05G006790' => 'cla', 'ClCG05G018150' => 'cla', 'ClCG09G000870' => 'cla', 'ClCG11G004900' => 'cla', 'COL.COLO4_03893' => 'col', 'COL.COLO4_21115' => 'col', 'COL.COLO4_30785' => 'col', 'COL.COLO4_34538' => 'col', 'Cpa.g.sc12.215' => 'cpa', 'Cpa.g.sc12.216' => 'cpa', 'Cpa.g.sc14.203' => 'cpa', 'Cpa.g.sc25.94' => 'cpa', 'Cre02.g092050' => 'cre', 'CsaV3_3G015440' => 'csa', 'CsaV3_4G035910' => 'csa', 'CsaV3_5G038630' => 'csa', 'CsaV3_7G034600' => 'csa', 'CSS0004119' => 'camsi', 'CSS0010454' => 'camsi', 'CSS0016491' => 'camsi', 'CSS0019186' => 'camsi', 'CSS0019240' => 'camsi', 'CSS0020301' => 'camsi', 'CSS0021371' => 'camsi', 'CSS0023341' => 'camsi', 'CSS0031303' => 'camsi', 'CSS0042480' => 'camsi', 'CSS0049753' => 'camsi', 'DCAR_003144' => 'dca', 'DCAR_004391' => 'dca', 'DCAR_021651' => 'dca', 'DCAR_023381' => 'dca', 'DCAR_023427' => 'dca', 'DCAR_025445' => 'dca', 'DCAR_026395' => 'dca', 'Dinv04020' => 'din', 'Dinv05115' => 'din', 'Dinv29535' => 'din', 'Dinv33852' => 'din', 'Dinv34920' => 'din', 'Dinv37880' => 'din', 'Dinv41830' => 'din', 'Duzib138G0811' => 'dzi', 'Duzib150G1476' => 'dzi', 'Duzib160G0637' => 'dzi', 'Duzib168G0879' => 'dzi', 'Duzib187G0648' => 'dzi', 'Duzib211G0086' => 'dzi', 'Duzib212G0570' => 'dzi', 'Duzib235G0316' => 'dzi', 'ECA232G0285' => 'eca', 'ECA232G1888' => 'eca', 'ECA234G1785' => 'eca', 'ECA236G0134' => 'eca', 'ECA240G3604' => 'eca', 'EL10Ac2g03805' => 'bvu', 'EL10Ac2g04455' => 'bvu', 'EL10Ac2g04456' => 'bvu', 'EL10Ac3g06281' => 'bvu', 'EL10Ac7g16391' => 'bvu', 'Eucgr.B02210' => 'egr', 'Eucgr.C03092' => 'egr', 'Eucgr.C03127' => 'egr', 'Eucgr.C03145' => 'egr', 'Eucgr.C03251' => 'egr', 'Eucgr.J01391' => 'egr', 'Eucgr.J02834' => 'egr', 'FAN02G3819' => 'fan', 'FAN05G0525' => 'fan', 'FAN05G5122' => 'fan', 'FAN07G2453' => 'fan', 'FAN09G0051' => 'fan', 'FAN14G3232' => 'fan', 'FAN15G2619' => 'fan', 'FAN17G1976' => 'fan', 'FAN20G1372' => 'fan', 'FAN24G0822' => 'fan', 'FAN27G2496' => 'fan', 'FvH4_2g31290' => 'fve', 'FvH4_4g21050' => 'fve', 'FvH4_6g34310' => 'fve', 'FvH4_6g46540' => 'fve', 'Glyma.04G054600' => 'gma', 'Glyma.06G054800' => 'gma', 'Glyma.07G035900' => 'gma', 'Glyma.08G249600' => 'gma', 'Glyma.09G031000' => 'gma', 'Glyma.13G053400' => 'gma', 'Glyma.15G027200' => 'gma', 'Glyma.16G005200' => 'gma', 'Glyma.17G225100' => 'gma', 'Glyma.18G271700' => 'gma', 'Glyma.19G033300' => 'gma', 'Glyma.20G016000' => 'gma', 'Gohir.A05G039800' => 'ghi', 'Gohir.A05G137300' => 'ghi', 'Gohir.A06G084900' => 'ghi', 'Gohir.A06G192600' => 'ghi', 'Gohir.A08G051800' => 'ghi', 'Gohir.A09G067000' => 'ghi', 'Gohir.A13G187900' => 'ghi', 'Gohir.D05G041300' => 'ghi', 'Gohir.D05G139300' => 'ghi', 'Gohir.D06G084100' => 'ghi', 'Gohir.D06G200500' => 'ghi', 'Gohir.D08G061500' => 'ghi', 'Gohir.D09G066600' => 'ghi', 'Gohir.D13G194800' => 'ghi', 'Gorai.004G063500' => 'gra', 'Gorai.006G081100' => 'gra', 'Gorai.009G041800' => 'gra', 'Gorai.009G143700' => 'gra', 'Gorai.010G097600' => 'gra', 'Gorai.010G234000' => 'gra', 'Gorai.013G220800' => 'gra', 'GSVIVG01017653001' => 'vvi', 'GSVIVG01035441001' => 'vvi', 'GSVIVG01036567001' => 'vvi', 'HanXRQChr02g0050991' => 'han', 'HanXRQChr09g0248081' => 'han', 'HanXRQChr09g0264901' => 'han', 'HanXRQChr09g0264911' => 'han', 'HanXRQChr09g0276671' => 'han', 'HanXRQChr10g0291561' => 'han', 'HanXRQChr10g0309821' => 'han', 'HanXRQChr12g0358811' => 'han', 'HanXRQChr13g0390931' => 'han', 'HanXRQChr15g0489121' => 'han', 'HanXRQChr16g0507391' => 'han', 'Haze_00802' => 'cav', 'Haze_14397' => 'cav', 'Haze_16006' => 'cav', 'Haze_18134' => 'cav', 'Hma1.2p1_0291F.1_g115270' => 'hma', 'Hma1.2p1_0496F.1_g166110' => 'hma', 'HPP92_006150' => 'vpl', 'HPP92_017024' => 'vpl', 'HPP92_019343' => 'vpl', 'HPP92_027845' => 'vpl', 'Hund13685' => 'sun', 'Hund16217' => 'sun', 'Lalb_Chr08g0244881' => 'lal', 'Lalb_Chr11g0063281' => 'lal', 'Lalb_Chr17g0336861' => 'lal', 'Lalb_Chr18g0058391' => 'lal', 'Lalb_Chr18g0058401' => 'lal', 'Lalb_Chr21g0318301' => 'lal', 'Lalb_Chr22g0351981' => 'lal', 'Lj1g0010520' => 'lja', 'Lj1g0011486' => 'lja', 'Lj2g0009001' => 'lja', 'Lj3A838T62' => 'lonja', 'Lj3g0004484' => 'lja', 'Lj4C121T24' => 'lonja', 'Lj5g0024850' => 'lja', 'Lj6g0019071' => 'lja', 'Lj7P239T43' => 'lonja', 'Lj7P245T46' => 'lonja', 'Lj9P522T21' => 'lonja', 'Lju2039C0T1' => 'lonja', 'Lsat_1_v5_gn_4_173201' => 'lsa', 'Lsat_1_v5_gn_4_95040' => 'lsa', 'Lsat_1_v5_gn_5_78781' => 'lsa', 'Lsat_1_v5_gn_7_60120' => 'lsa', 'Lsat_1_v5_gn_8_99301' => 'lsa', 'Manes.02G058000' => 'mes', 'Manes.03G051800' => 'mes', 'Manes.11G022600' => 'mes', 'Manes.15G003400' => 'mes', 'Manes.16G083800' => 'mes', 'Mapoly0099s0010' => 'mpo', 'MBI16_g03099_MAGBIO' => 'mbi', 'MBI18_g09650_MAGBIO' => 'mbi', 'MBI18_g11538_MAGBIO' => 'mbi', 'MBI19_g19954_MAGBIO' => 'mbi', 'MCO10G122' => 'mco', 'MCO10G174' => 'mco', 'MD08G1069000' => 'mdo', 'MD09G1072700' => 'mdo', 'MD09G1186900' => 'mdo', 'MD13G1144600' => 'mdo', 'MD15G1053000' => 'mdo', 'MD17G1063900' => 'mdo', 'Medtr2g032610' => 'mtr', 'Medtr3g104810' => 'mtr', 'Medtr6g015860' => 'mtr', 'Medtr7g015870' => 'mtr', 'Medtr8g019480' => 'mtr', 'MELO3C006743.2' => 'cme', 'MELO3C016899.2' => 'cme', 'MELO3C022043.2' => 'cme', 'MELO3C024366.2' => 'cme', 'Migut.A00094' => 'egut', 'Migut.E01577' => 'egut', 'Migut.H00602' => 'egut', 'Migut.I01057' => 'egut', 'Migut.N00016' => 'egut', 'Migut.O00388' => 'egut', 'MSTRG.14064' => 'ama', 'MSTRG.15440' => 'ama', 'MSTRG.1690' => 'ama', 'MSTRG.22557' => 'ama', 'MSTRG.24835' => 'ama', 'MSTRG.24836' => 'ama', 'MSTRG.25979' => 'ama', 'MSTRG.2983' => 'ama', 'Nitab4.5_0000738g0080' => 'nta', 'Nitab4.5_0002879g0010' => 'nta', 'Nitab4.5_0003874g0030' => 'nta', 'Nitab4.5_0005120g0050' => 'nta', 'Nitab4.5_0006105g0040' => 'nta', 'Nitab4.5_0009044g0010' => 'nta', 'Nitab4.5_0009612g0010' => 'nta', 'Nitab4.5_0012533g0010' => 'nta', 'Nn3g17494' => 'nnu', 'Nn4g25449' => 'nnu', 'Nn6g35573' => 'nnu', 'Nn8g38743' => 'nnu', 'Oeu022693.2' => 'oeu', 'Oeu027277.1' => 'oeu', 'Oeu039941.1' => 'oeu', 'Oeu047082.1' => 'oeu', 'Oeu062172.2' => 'oeu', 'Os01g0329400' => 'osa', 'Os03g0175200' => 'osa', 'Os03g0754800' => 'osa', 'Os09g0444700' => 'osa', 'Os10g0397800' => 'osa', 'Peaxi162Scf00038g00177' => 'pax', 'Peaxi162Scf00064g00181' => 'pax', 'Peaxi162Scf00126g01228' => 'pax', 'Peaxi162Scf00166g00336' => 'pax', 'Peaxi162Scf00809g00002' => 'pax', 'PGR031G3246' => 'pgr', 'PGR042G3873' => 'pgr', 'PGR044G2536' => 'pgr', 'PGR102G0427' => 'pgr', 'PGSC0003DMG400001464' => 'stu', 'PGSC0003DMG400029386' => 'stu', 'PGSC0003DMG400038452' => 'stu', 'PGSC0003DMG400041751' => 'stu', 'PGSC0003DMG400046804' => 'stu', 'Phvul.001G039600' => 'pvu', 'Phvul.004G041200' => 'pvu', 'Phvul.006G122100' => 'pvu', 'Phvul.008G029300' => 'pvu', 'Phvul.009G080300' => 'pvu', 'Phvul.010G133600' => 'pvu', 'Potri.004G117000' => 'ptr', 'Potri.006G223600' => 'ptr', 'Potri.008G100100' => 'ptr', 'Potri.017G098500' => 'ptr', 'Potri.018G050300' => 'ptr', 'Pp3c1_18190' => 'ppa', 'Pp3c1_18200' => 'ppa', 'Pp3c6_11230' => 'ppa', 'PRCOL_00001452' => 'pco', 'Prupe.1G109500' => 'ppe', 'Prupe.1G406900' => 'ppe', 'Prupe.3G044100' => 'ppe', 'Prupe.3G250600' => 'ppe', 'Psat1g066440' => 'psa', 'Psat1g163120' => 'psa', 'Psat3g185200' => 'psa', 'Psat3g204440' => 'psa', 'Psat4g183760' => 'psa', 'Psat5g035160' => 'psa', 'PSO017G0876' => 'pso', 'PSO063G3589' => 'pso', 'PSO210G0905' => 'pso', 'PSO210G2483' => 'pso', 'PSO421G0220' => 'pso', 'PSO478G4607' => 'pso', 'PSO729G0251' => 'pso', 'QL02p000371' => 'qlo', 'QL02p066317' => 'qlo', 'QL05p008756' => 'qlo', 'QL06p013675' => 'qlo', 'RcHm_v2.0_Chr2g0144681' => 'rch', 'RcHm_v2.0_Chr2g0165181' => 'rch', 'RcHm_v2.0_Chr4g0426581' => 'rch', 'RcHm_v2.0_Chr6g0311501' => 'rch', 'Rhsim04G0245800' => 'rsi', 'Rhsim04G0246300' => 'rsi', 'Rhsim08G0076000' => 'rsi', 'Rhsim12G0208600' => 'rsi', 'Sabra04G0070400' => 'sbr', 'Sabra06G0172700' => 'sbr', 'Sabra17G0084900' => 'sbr', 'Sabra18G0047300' => 'sbr', 'SabraUnG0000600' => 'sbr', 'SalBow1G3261' => 'sbo', 'SalBow1G8336' => 'sbo', 'SalBow4G2618' => 'sbo', 'SalBow6G3971' => 'sbo', 'Sc02g0003630' => 'sci', 'Sc11g0008730' => 'sci', 'Sc12g0010420' => 'sci', 'Sed0005943' => 'sed', 'Sed0006138' => 'sed', 'Sed0016825' => 'sed', 'Sed0026566' => 'sed', 'SEGI_03280' => 'sgi', 'SEGI_31207' => 'sgi', 'SEGI_34085' => 'sgi', 'SEGI_37705' => 'sgi', 'SGA_v2.0_scaffold123G33427' => 'sas', 'SGA_v2.0_scaffold148G36429' => 'sas', 'SGA_v2.0_scaffold163G38007' => 'sas', 'SGA_v2.0_scaffold169G38710' => 'sas', 'SGA_v2.0_scaffold4G02366' => 'sas', 'SHI00064' => 'shi', 'SHI09532' => 'shi', 'SMO117G0344' => 'smo', 'SMO139G0127' => 'smo', 'SMO147G0337' => 'smo', 'Solyc02g089110.3' => 'sly', 'Solyc03g121920.3' => 'sly', 'Solyc12g096030.1' => 'sly', 'Sopen01g022810' => 'spe', 'Sopen02g033900' => 'spe', 'Sopen03g040740' => 'spe', 'Sopen12g031920' => 'spe', 'Sp2g21550' => 'spa', 'Sp5g27860' => 'spa', 'Sp6g28470' => 'spa', 'TAR311G0003' => 'tar', 'TAR371G0587' => 'tar', 'TAR622G0294' => 'tar', 'TAR624G0941' => 'tar', 'TAR636G0900' => 'tar', 'TAR636G1538' => 'tar', 'TAR636G3221' => 'tar', 'THA.LOC104802981' => 'tha', 'THA.LOC104811227' => 'tha', 'THA.LOC104812229' => 'tha', 'THA.LOC104813951' => 'tha', 'THA.LOC104822318' => 'tha', 'Thecc.04G103800' => 'tca', 'Thecc.04G309400' => 'tca', 'Thecc.06G117200' => 'tca', 'Thecc.09G059900' => 'tca', 'Thhalv10004529m.g' => 'esa', 'Thhalv10014114m.g' => 'esa', 'Thhalv10019775m.g' => 'esa', 'TPR.G16440' => 'tpr', 'TPR.G23398' => 'tpr', 'TPR.G27524' => 'tpr', 'TPR.G3544' => 'tpr', 'TPR.G35930' => 'tpr', 'TWI32G1330' => 'twi', 'TWI34G1457' => 'twi', 'TWI34G1981' => 'twi', 'TWI53G0223' => 'twi', 'TWI60G0614' => 'twi', 'unitig_26.g10617' => 'ugi', 'unitig_26.g9801' => 'ugi', 'unitig_46.g17901' => 'ugi', 'unitig_62.g23388' => 'ugi', 'unitig_8.g5055' => 'ugi', 'unitig_899.g15106' => 'ugi', 'vmacro07992' => 'vma', 'vmacro17046' => 'vma', 'vmacro18137' => 'vma', 'VMungo0331G1066' => 'vmu', 'VMungo0464G1616' => 'vmu', 'VMungo0540G1387' => 'vmu', 'VMungo0647G0367' => 'vmu', 'VMungo1346G0001' => 'vmu', 'VMungo1383G3333' => 'vmu', 'Zm00001eb005700' => 'zma', 'Zm00001eb057590' => 'zma', 'Zm00001eb100350' => 'zma', 'Zm00001eb131100' => 'zma', 'Zm00001eb223450' => 'zma', 'Zm00001eb340650' => 'zma', 'Zm00001eb402010' => 'zma' ) $gf_id = 'ORTHO05D001059' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001059' ) $data_identifier = 'ORTHO05D001059' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 11, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 7, 'fan' => (int) 11, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 6, 'ama' => (int) 8, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 5, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 5, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb402010' $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